RetrogeneDB ID: retro_cjac_1612

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:67391485..67391793(-)
• Located in intron of: ENSCJAG00000012388

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007952
• Aliases: None
• Description: None

Sequence

>retro_cjac_1612
AGACAATGGGAAAGTGGAGTATTTCCTTACTTCCTCACCAGAGGGCATTTACAGATGCTGACAATGCTTGGGAACCTGAA
GAAAATTTAGATTCTCCAGAGTGAATTGAAGCATTTATAATTCTCAAATTAAGTAAGAAAAGGATGGCACAAAATACCTT
ATCTGACAGTGAATCTGATGACAGTAAATCAAAGAAGGAAAGAGATGCTACTGAGAAACCAAGAGAGCTTGTTAGCGGTC
TTAATCCTGAAGGAATAATTGGTGCCACAGACAGCAGTGGAGAATCGATACTTCTCACGAGATTCAGA

Alignment

ORF - retro_cjac_1612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.96 %
• Parental protein coverage: 57.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RRVVNGKVEYFLK-WKGFTDADNTWEPEENLDCPELIEAFL-NSQKAGKEKDGTK-RKSLSDSESDDSKS
          R....G...YFL.....FTDADN.WEPEENLD.PE.IEAF..NSQ....EKDGTK...S.S.S....S..
Retrocopy RQWESGVFPYFLT<QRAFTDADNAWEPEENLDSPE*IEAFI<NSQ-IK*EKDGTK>TLSDSESDDSKS--

Parental  KKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWK
          KK.RDA..KPR....GL.PE.IIGATDSSGE...L....
Retrocopy KKERDATEKPRELVSGLNPEGIIGATDSSGESILLTRFR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.44 RPM	39.74 RPM
SRP051959_heart	0.18 RPM	30.54 RPM
SRP051959_kidney	0.13 RPM	46.92 RPM
SRP051959_liver	0.04 RPM	32.19 RPM
SRP051959_lung	0.47 RPM	41.09 RPM
SRP051959_lymph_node	0.91 RPM	47.56 RPM
SRP051959_skeletal_muscle	0.04 RPM	16.42 RPM
SRP051959_spleen	0.48 RPM	40.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1612 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1612 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2771
Pan troglodytes	retro_ptro_1875
Gorilla gorilla	retro_ggor_1928
Pongo abelii	retro_pabe_2243

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005969	1 retrocopy	retro_amel_1184,
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Callithrix jacchus	ENSCJAG00000007532	2 retrocopies	retro_cjac_191, retro_cjac_51,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612 , retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Callithrix jacchus	ENSCJAG00000018847	1 retrocopy	retro_cjac_2020,
Dipodomys ordii	ENSDORG00000005487	11 retrocopies	retro_dord_309, retro_dord_405, retro_dord_437, retro_dord_440, retro_dord_456, retro_dord_502, retro_dord_629, retro_dord_630, retro_dord_655, retro_dord_700, retro_dord_780,
Equus caballus	ENSECAG00000012780	1 retrocopy	retro_ecab_784,
Gorilla gorilla	ENSGGOG00000025853	6 retrocopies	retro_ggor_1928, retro_ggor_2281, retro_ggor_2466, retro_ggor_2467, retro_ggor_635, retro_ggor_845,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Myotis lucifugus	ENSMLUG00000007591	2 retrocopies	retro_mluc_2486, retro_mluc_813,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Procavia capensis	ENSPCAG00000004904	2 retrocopies	retro_pcap_108, retro_pcap_166,
Pongo abelii	ENSPPYG00000017714	10 retrocopies	retro_pabe_2112, retro_pabe_2243, retro_pabe_2724, retro_pabe_2770, retro_pabe_2997, retro_pabe_3608, retro_pabe_758, retro_pabe_786, retro_pabe_892, retro_pabe_951,
Pan troglodytes	ENSPTRG00000019003	10 retrocopies	retro_ptro_17, retro_ptro_1706, retro_ptro_1875, retro_ptro_2289, retro_ptro_2475, retro_ptro_395, retro_ptro_537, retro_ptro_630, retro_ptro_729, retro_ptro_780,
Pteropus vampyrus	ENSPVAG00000006297	2 retrocopies	retro_pvam_294, retro_pvam_786,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,
Ictidomys tridecemlineatus	ENSSTOG00000006223	4 retrocopies	retro_itri_1093, retro_itri_1682, retro_itri_1764, retro_itri_912,
Tarsius syrichta	ENSTSYG00000008159	6 retrocopies	retro_tsyr_1459, retro_tsyr_1545, retro_tsyr_1552, retro_tsyr_1645, retro_tsyr_203, retro_tsyr_583,
Tursiops truncatus	ENSTTRG00000000711	7 retrocopies	retro_ttru_1238, retro_ttru_1247, retro_ttru_1851, retro_ttru_294, retro_ttru_52, retro_ttru_591, retro_ttru_644,